Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...accatatgatggttgcctttgtcttcgatgaaatttggatttgaggcgacgtttttattttaacactcattgtttgattggtggcttgatatgatcaaagGGATCATGCCGGTGGAAACGAGAAGATTAAGCAGTTGGTTCCTGATATCAAAGTATATGGAGGTTCTCTGGATAAGGTGAAGGGTTGCACTGATGCGGTT

Basic information

species Arabidopsis thaliana
transcript AT3G10850.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G10850.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA14G36610.2 (Glycine max), 3'ss of exon 2
accatatgatggttgcctttgtcttcgatgaaatttggatttgaggcgacgtttttattttaacactcattgtttgattggtggcttgatatgatcaaagGGATCATGCCGGTGGAAACGAGAAGATTAAGCAGTTGGTTCCTGATATCAAAGTATATGGAGGTTCTCTGGATAAGGTGAAGGGTTGCACTGATGCGGTT
        |||||  |||||    || |  |  | |   ||  | |  || | || | | |     |  || |||          || || |||    ||||||||||| ||||||||||| ||||| |||||| |||| || |  |||||||| ||||| |||||  | || || || ||||||||||||||    |||
------gtatggtacccttt----tcaaccacctct---ttctaagtaacttgttcactatgttgttttttttttt--------ttttatgtgac---agGGATCATGCTGGTGGAAACGACAAGATAAAGCAGCTGGTGCCAGGAATCAAAGTCTATGGTGGTTCCATTGAAAACGTCAAGGGTTGCACTGACAAAGTT
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|19876010|gb|AU236841.1|AU236841
EST:     GAGAAGCACCAAGCTAAGATCAAGTTCGTACTCACTACGCATCATCACTG                         GGATCATGCCGGTGGAAACGAGAAGATTAAGCAGTTGGTTCCTGATATCAA
genomic: GAGAAGCACCAAGCTAAGATCAAGTTCGTACTCACTACGCATCATCACTGgtaagtaaac ... atgatcaaagGGATCATGCCGGTGGAAACGAGAAGATTAAGCAGTTGGTTCCTGATATCAA
EST: gi|86023772|gb|DR319525.1|DR319525
EST:     GAGAAGCACCAAGCTAAGATCAAGTTCGTACTCACTACGCATCATCACTG                         GGATCATGCCGGTGGAAACGAGAAGATTAAGCAGTTGGTTCCTGATATCAA
genomic: GAGAAGCACCAAGCTAAGATCAAGTTCGTACTCACTACGCATCATCACTGgtaagtaaac ... atgatcaaagGGATCATGCCGGTGGAAACGAGAAGATTAAGCAGTTGGTTCCTGATATCAA
EST: gi|164235212|gb|ES070634.1|ES070634
EST:     GATCAAGTTCGTACTCACTACGCATCATCACTG                         GGATCATGCCGGTGGAAACGAGAAGATTAAGCAGTTGGTTCCTGATATCAA
genomic: GATCAAGTTCGTACTCACTACGCATCATCACTGgtaagtaaac ... atgatcaaagGGATCATGCCGGTGGAAACGAGAAGATTAAGCAGTTGGTTCCTGATATCAA
EST: gi|124741549|gb|EH832711.1|EH832711
EST:     ATCAAGTTCGTACTCACTACGCATCATCACTG                         GGATCATGCCGGTGGAAACGAGAAGATTAAGCAGTTGGTTCCTGATATCAA
genomic: ATCAAGTTCGTACTCACTACGCATCATCACTGgtaagtaaac ... atgatcaaagGGATCATGCCGGTGGAAACGAGAAGATTAAGCAGTTGGTTCCTGATATCAA
EST: gi|152038306|gb|BP813348.2|BP813348
EST:     GAGAAGCACCAAGCTAAGATCAAGTTCGTACTCACTACGCATCATCACTG                         GGATCATGCCGGTGGAAACGAGAAGATTAAGCAGTTGGT-CCTGATATCAA
genomic: GAGAAGCACCAAGCTAAGATCAAGTTCGTACTCACTACGCATCATCACTGgtaagtaaac ... atgatcaaagGGATCATGCCGGTGGAAACGAGAAGATTAAGCAGTTGGTTCCTGATATCAA
EST: gi|86023773|gb|DR319526.1|DR319526
EST:     GAGAAGCACCAAGCTAAGATCAAGTTCGTACTCACTACGCATCATCACTG                         GGATCATGCCGGTGGAAACGAGAAGATTAAGCAGTTGGTTCCTGATATCAA
genomic: GAGAAGCACCAAGCTAAGATCAAGTTCGTACTCACTACGCATCATCACTGgtaagtaaac ... atgatcaaagGGATCATGCCGGTGGAAACGAGAAGATTAAGCAGTTGGTTCCTGATATCAA
EST: gi|152035101|gb|BP844575.2|BP844575
EST:     GAGAAGCACCAAGCTAAGATCAAGTTCGTACTCACTACGCATCATCACTG                         GGATCATGCCGGTGGAAACGAGAAGATTAAGCAGTTGGTTCCTGATATCAA
genomic: GAGAAGCACCAAGCTAAGATCAAGTTCGTACTCACTACGCATCATCACTGgtaagtaaac ... atgatcaaagGGATCATGCCGGTGGAAACGAGAAGATTAAGCAGTTGGTTCCTGATATCAA
EST: gi|86027937|gb|DR323690.1|DR323690
EST:     GAGAAGCACCAAGCTAAGATCAAGTTCGTACTCACTACGCATCATCACTG                         GGATCATGCCGGTGGAAACGAGAAGATTAAGCAGTTGGTTCCTGATATCAA
genomic: GAGAAGCACCAAGCTAAGATCAAGTTCGTACTCACTACGCATCATCACTGgtaagtaaac ... atgatcaaagGGATCATGCCGGTGGAAACGAGAAGATTAAGCAGTTGGTTCCTGATATCAA
EST: gi|124770984|gb|EH861114.1|EH861114
EST:     CTACGCATCATCACTG                         GGATCATGCCGGTGGAAACGAGAAGATTAAGCAGTTGGTTCCTGATATCAA
genomic: CTACGCATCATCACTGgtaagtaaac ... atgatcaaagGGATCATGCCGGTGGAAACGAGAAGATTAAGCAGTTGGTTCCTGATATCAA
EST: gi|124805881|gb|EH893028.1|EH893028
EST:     GAGAAGCACCAAGCTAAGATCAAGTTCGTACTCACTACGCATCATCACTG                         GGATCATGCCGGTGGA
genomic: GAGAAGCACCAAGCTAAGATCAAGTTCGTACTCACTACGCATCATCACTGgtaagtaaac ... atgatcaaagGGATCATGCCGGTGGA
EST: gi|152035013|gb|BP842123.2|BP842123
EST:     GAGAAGCACCAAGCTAAGATCAAGT-CGTACTCACTACGCATCATCACTG                         GGATCATGCCGGTGGAAACGAGAAGATTAAGCAGTTGGTTCCTGATATCAA
genomic: GAGAAGCACCAAGCTAAGATCAAGTTCGTACTCACTACGCATCATCACTGgtaagtaaac ... atgatcaaagGGATCATGCCGGTGGAAACGAGAAGATTAAGCAGTTGGTTCCTGATATCAA
EST: gi|86023775|gb|DR319528.1|DR319528
EST:     GAGAAGCACCAAGCTGAGATCAAGTTCGTACTCACTACGCATCATCACTG                         GGATCATGCCGGTGGAAACGAGAAGATTAAGCAGTTGGTTCCTGATATCAA
genomic: GAGAAGCACCAAGCTAAGATCAAGTTCGTACTCACTACGCATCATCACTGgtaagtaaac ... atgatcaaagGGATCATGCCGGTGGAAACGAGAAGATTAAGCAGTTGGTTCCTGATATCAA
EST: gi|124974888|gb|EL048421.1|EL048421
EST:     GAGAAGCACCAAGCTAAGATCAAGTTCGTACTCACTACGCATCATCACTG                         GGATCATGCCGGTGGAAACGAGAAGATTAAGCA
genomic: GAGAAGCACCAAGCTAAGATCAAGTTCGTACTCACTACGCATCATCACTGgtaagtaaac ... atgatcaaagGGATCATGCCGGTGGAAACGAGAAGATTAAGCA
EST: gi|86023774|gb|DR319527.1|DR319527
EST:     GAGAAGCACCAAGCTAAGATCAAGTTCGTACTCACTACGCATCATCACTG                         GGATCATGCCGGTGGAAACGAGAAGATTAAGCAGTTGGTTCCTGATATCAA
genomic: GAGAAGCACCAAGCTAAGATCAAGTTCGTACTCACTACGCATCATCACTGgtaagtaaac ... atgatcaaagGGATCATGCCGGTGGAAACGAGAAGATTAAGCAGTTGGTTCCTGATATCAA
EST: gi|125153657|gb|EL184694.1|EL184694
EST:     CGTACTCACTACGCATCTTTACTG                         GGATCATGCCGGTGGAAACGAGAAGATTAAGCAGTTGGTTCCTGATATCAA
genomic: CGTACTCACTACGCATCATCACTGgtaagtaaac ... atgatcaaagGGATCATGCCGGTGGAAACGAGAAGATTAAGCAGTTGGTTCCTGATATCAA
EST: gi|152034408|gb|BP827689.2|BP827689
EST:     GAGAAGCACCAAGCTAAGATCAAGTTCGTACTCACTACGCATCATCACTG                         GGATCATGCCGGTGGAAACGAGAAGATTAAGCAGTTGGTTCCTGATATCAA
genomic: GAGAAGCACCAAGCTAAGATCAAGTTCGTACTCACTACGCATCATCACTGgtaagtaaac ... atgatcaaagGGATCATGCCGGTGGAAACGAGAAGATTAAGCAGTTGGTTCCTGATATCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcgacgtttttattttaacactcattgtttgattggtggcttgatatgatcaaagGGATCATGCCGGTGGAAACGAGAAGATTAAGCAGTTGGTTCCTGATATCAAAGTATATGGAGGTTCTCTGGATAAGGTGAAGGGTTGCACTGATGCGGTT
      tttttattttaacact  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
accatatgatggttgcctttgtcttcgatgaaatttggatttgaggcgacgtttttattttaacactcattgtttgattggtggcttgatatgatcaaagGGATCATGCCGGTGGAAACGAGAAGATTAAGCAGTTGGTTCCTGATATCAAAGTATATGGAGGTTCTCTGGATAAGGTGAAGGGTTGCACTGATGCGGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - gatgaaa
- - - - - - - - - - - - - - - - - - -gatttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acactca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtttga